Telomere-to-telomere genome of Phoebe chekiangensis reveals age-dependent CHG hypomethylation promoting floral transition via MADS-box gene activation

Phoebe species are valued for their "golden-thread" wood. Among them, the early-flowering Phoebe chekiangensis serves as an excellent model for studying the transition from vegetative to reproductive growth. However, the lack of a high-quality genome has hindered molecular studies. Here, we present a telomere-to-telomere (T2T) genome assembly of P. chekiangensis. The assembly comprises two gap-free haplotypes with approximately 29,000 high-confidence genes and species-specific telomeric repeats. Age-dependent transcriptome profiling identified PcMADS5 and PcMADS19.1 as central flowering regulators. Their ectopic expression in Arabidopsis significantly accelerated flowering. Whole-genome bisulfite sequencing revealed an age-related decrease in CHG methylation, particularly at the PcMADS19.1 locus. Treatment with the DNA demethylating agent 5-azacytidine reduced CHG methylation at PcMADS19.1 and enhanced its expression, suggesting that CHG demethylation directly activates this gene. This study provides the first T2T genome for Phoebe and unveils CHG hypomethylation as an epigenetic mechanism that activates key regulators of the vegetative-to-reproductive transition.